chr20-43406210-A-C

Variant names:

• chr20-43406210-A-C
• rs6030844
• ENST00000731882.1:n.447-16939T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000731882.1(ENSG00000295701):​n.447-16939T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,088 control chromosomes in the GnomAD database, including 6,024 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6024 hom., cov: 32)
• Consequence: ENSG00000295701 ENST00000731882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736
• Publications: 2 publications found

Genes affected

ENSG00000295701 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731882.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295701	ENST00000731882.1		n.447-16939T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42523 AN: 151970 Hom.: 5995 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.288

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42594 AN: 152088 Hom.: 6024 Cov.: 32 AF XY: 0.274 AC XY: 20406 AN XY: 74340

African (AFR) AF: 0.312 AC: 12953 AN: 41498

American (AMR) AF: 0.215 AC: 3291 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3472

East Asian (EAS) AF: 0.147 AC: 760 AN: 5176

South Asian (SAS) AF: 0.159 AC: 768 AN: 4822

European-Finnish (FIN) AF: 0.280 AC: 2954 AN: 10564

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19967 AN: 67962

Other (OTH) AF: 0.286 AC: 606 AN: 2116

Alfa AF: 0.288 Hom.: 1161

Bravo AF: 0.278

Asia WGS AF: 0.158 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.2
DANN	Benign	0.48
PhyloP100		0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6030844; hg19: chr20-42034850;